TOP1B_ARATH
ID TOP1B_ARATH Reviewed; 917 AA.
AC Q9FJ79;
DT 02-NOV-2016, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 25-MAY-2022, entry version 149.
DE RecName: Full=DNA topoisomerase 1 beta {ECO:0000305};
DE EC=5.6.2.1 {ECO:0000255|PROSITE-ProRule:PRU10130};
DE AltName: Full=DNA topoisomerase 1 {ECO:0000305};
GN Name=TOP1B {ECO:0000305};
GN Synonyms=TOP1 {ECO:0000305}, TOP1BETA {ECO:0000303|PubMed:12215507};
GN OrderedLocusNames=At5g55310 {ECO:0000312|Araport:AT5G55310};
GN ORFNames=MTE17.2 {ECO:0000312|EMBL:BAB08548.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9872454; DOI=10.1093/dnares/5.5.297;
RA Nakamura Y., Sato S., Asamizu E., Kaneko T., Kotani H., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. VII. Sequence
RT features of the regions of 1,013,767 bp covered by sixteen physically
RT assigned P1 and TAC clones.";
RL DNA Res. 5:297-308(1998).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP FUNCTION.
RX PubMed=12215507; DOI=10.1105/tpc.001925;
RA Takahashi T., Matsuhara S., Abe M., Komeda Y.;
RT "Disruption of a DNA topoisomerase I gene affects morphogenesis in
RT Arabidopsis.";
RL Plant Cell 14:2085-2093(2002).
RN [5]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-301, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
CC -!- FUNCTION: Releases the supercoiling and torsional tension of DNA
CC introduced during the DNA replication and transcription by transiently
CC cleaving and rejoining one strand of the DNA duplex. Introduces a
CC single-strand break via transesterification at a target site in duplex
CC DNA. The scissile phosphodiester is attacked by the catalytic tyrosine
CC of the enzyme, resulting in the formation of a DNA-(3'-phosphotyrosyl)-
CC enzyme intermediate and the expulsion of a 5'-OH DNA strand. The free
CC DNA strand then rotates around the intact phosphodiester bond on the
CC opposing strand, thus removing DNA supercoils. Finally, in the
CC religation step, the DNA 5'-OH attacks the covalent intermediate to
CC expel the active-site tyrosine and restore the DNA phosphodiester
CC backbone (By similarity). Topoisomerases 1 enzymes (TOP1A and TOP1B)
CC are essential for plant survival (PubMed:12215507).
CC {ECO:0000250|UniProtKB:P11387, ECO:0000269|PubMed:12215507}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP-independent breakage of single-stranded DNA, followed by
CC passage and rejoining.; EC=5.6.2.1; Evidence={ECO:0000255|PROSITE-
CC ProRule:PRU10130};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the type IB topoisomerase family. {ECO:0000305}.
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DR EMBL; AB015479; BAB08548.1; -; Genomic_DNA.
DR EMBL; CP002688; AED96615.1; -; Genomic_DNA.
DR EMBL; AK226832; BAE98926.1; -; mRNA.
DR RefSeq; NP_200342.1; NM_124913.4.
DR AlphaFoldDB; Q9FJ79; -.
DR SMR; Q9FJ79; -.
DR STRING; 3702.AT5G55310.1; -.
DR iPTMnet; Q9FJ79; -.
DR PaxDb; Q9FJ79; -.
DR PRIDE; Q9FJ79; -.
DR ProteomicsDB; 232439; -.
DR EnsemblPlants; AT5G55310.1; AT5G55310.1; AT5G55310.
DR GeneID; 835624; -.
DR Gramene; AT5G55310.1; AT5G55310.1; AT5G55310.
DR KEGG; ath:AT5G55310; -.
DR Araport; AT5G55310; -.
DR TAIR; locus:2173862; AT5G55310.
DR eggNOG; KOG0981; Eukaryota.
DR HOGENOM; CLU_009193_1_2_1; -.
DR InParanoid; Q9FJ79; -.
DR OMA; GLRYQKW; -.
DR OrthoDB; 303947at2759; -.
DR PhylomeDB; Q9FJ79; -.
DR PRO; PR:Q9FJ79; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9FJ79; baseline and differential.
DR GO; GO:0005694; C:chromosome; IEA:InterPro.
DR GO; GO:0005730; C:nucleolus; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003917; F:DNA topoisomerase type I (single strand cut, ATP-independent) activity; ISS:TAIR.
DR GO; GO:0007059; P:chromosome segregation; IBA:GO_Central.
DR GO; GO:0006260; P:DNA replication; IBA:GO_Central.
DR GO; GO:0006265; P:DNA topological change; IBA:GO_Central.
DR CDD; cd00659; Topo_IB_C; 1.
DR Gene3D; 1.10.10.41; -; 1.
DR Gene3D; 1.10.132.10; -; 1.
DR Gene3D; 2.170.11.10; -; 1.
DR Gene3D; 3.90.15.10; -; 1.
DR InterPro; IPR011010; DNA_brk_join_enz.
DR InterPro; IPR013034; DNA_topo_DNA_db_N_dom1.
DR InterPro; IPR013030; DNA_topo_DNA_db_N_dom2.
DR InterPro; IPR001631; TopoI.
DR InterPro; IPR018521; TopoI_AS.
DR InterPro; IPR025834; TopoI_C_dom.
DR InterPro; IPR014711; TopoI_cat_a-hlx-sub_euk.
DR InterPro; IPR014727; TopoI_cat_a/b-sub_euk.
DR InterPro; IPR013500; TopoI_cat_euk.
DR InterPro; IPR008336; TopoI_DNA-bd_euk.
DR InterPro; IPR036202; TopoI_DNA-bd_euk_N_sf.
DR InterPro; IPR013499; TopoI_euk.
DR Pfam; PF14370; Topo_C_assoc; 1.
DR Pfam; PF01028; Topoisom_I; 1.
DR Pfam; PF02919; Topoisom_I_N; 1.
DR PRINTS; PR00416; EUTPISMRASEI.
DR SMART; SM00435; TOPEUc; 1.
DR SUPFAM; SSF56349; SSF56349; 1.
DR SUPFAM; SSF56741; SSF56741; 1.
DR PROSITE; PS00176; TOPOISOMERASE_I_EUK; 1.
PE 1: Evidence at protein level;
KW Coiled coil; DNA-binding; Isomerase; Nucleus; Phosphoprotein;
KW Reference proteome; Topoisomerase.
FT CHAIN 1..917
FT /note="DNA topoisomerase 1 beta"
FT /id="PRO_0000438099"
FT REGION 1..368
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 575..576
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P11387"
FT REGION 638..643
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P11387"
FT REGION 729..731
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P11387"
FT COILED 779..858
FT /evidence="ECO:0000255"
FT COMPBIAS 32..99
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 123..147
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 148..174
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 188..208
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 239..255
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 297..311
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 312..344
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 354..368
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 870
FT /note="O-(3'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10130"
FT SITE 464
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P11387"
FT SITE 512
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P11387"
FT SITE 561
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P11387"
FT SITE 593
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P11387"
FT SITE 650
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P11387"
FT SITE 676
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P11387"
FT SITE 718
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P11387"
FT SITE 775
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P11387"
FT SITE 793
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P11387"
FT MOD_RES 301
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19376835"
SQ SEQUENCE 917 AA; 103054 MW; 60665DB24510EDC1 CRC64;
MATEAFVKPV VPNGHDGYED EDEDDIPLVF KRNSNTAATT NRPSPINNAM RNSAIGSTKS
SPPMRSPLTS PNRSASSSTR SSMMKPALPS SSSVQRSTLK SPLRDDRSVV AKERNGFGKA
PSVSKSDDED SEDDKPLSAR LKLDSKEVTK QPSSSGRGST QQAVQKSNMR PQGLSDYTKK
KVLDERAPMS STVQTKTSVG TSSSKPVHIE QKRPLVNNID RNGLKPKTEG HSSQAPAKRP
LEKGSSSNQS SVKRPKLSEP ARPVKVEQGS HISATQDAKG KNLDASKPLR ANQATVKEDN
SDGDDHVPIA SRMKSDSSNN KSSSAKPSSS KMIASSSRTI AQKPNKWVKD SKYSKSSKSL
PSGDGQKKWK TLQHNGVIFP PPYKRHGVKI LFQGKPVDLT PEQEEVATMF AVMRETEYYK
KPKFRENFWN DWRKLLGKNH MIKSLDDCDF TPIYEWYMQE KETKKQMTAE EKRIVKEEKL
KQEEKYMWAV LDGVRERIGN FRVEPPGLFR GRGEHPKMGK LKKRIRPCDI TINIGKEAPI
PECPIPGERW KEVKHDNTVT WLAFWSDPIN PKEFKYVFLA ASSSLKGQSD KEKYEKARKL
HNHIGSIRAA YTKDFNNKDV TKRQIAVATY LIDKLALRAG NEKDDDEADT VGCCTLKVGN
VECIPPNKLK FDFLGKDSIQ YVNTVEVEPL VYKAIGQFQA GKSKTDDLFD ELDTSKLNTH
LKELMAGLTA KVFRTYNASI TLDLMLSKET RDGDVPEKVV VYQQANKEVA IICNHQRTVS
KSHGAQVEKL AVKIEELREQ IKELNIDLDR AKKGRTPLMG SDGKRKRNLT PEALEKKIMQ
TQGKIEKMER DMQTKEDMKT VALGTSKINY MDPRITVAWC KRHDVPIEKI FNKSLLAKFA
WAMDVDPEFR FCSSTDE
